{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8629CPYB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8629CPYB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8629CPYB](/measurement-sets/IGVFDS8629CPYB/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS8629CPYB/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8629CPYB](/measurement-sets/IGVFDS8629CPYB/) has sequence file(s) [IGVFFI8994EWVT](/sequence-files/IGVFFI8994EWVT/), [IGVFFI2651MBBL](/sequence-files/IGVFFI2651MBBL/), [IGVFFI7102LRYO](/sequence-files/IGVFFI7102LRYO/), [IGVFFI7634THJL](/sequence-files/IGVFFI7634THJL/), [IGVFFI8835LGFN](/sequence-files/IGVFFI8835LGFN/), [IGVFFI0604FIKB](/sequence-files/IGVFFI0604FIKB/), [IGVFFI1286NYQN](/sequence-files/IGVFFI1286NYQN/), [IGVFFI9104WBGE](/sequence-files/IGVFFI9104WBGE/), [IGVFFI6520TEPW](/sequence-files/IGVFFI6520TEPW/), [IGVFFI9851JPHD](/sequence-files/IGVFFI9851JPHD/), [IGVFFI0161OWBW](/sequence-files/IGVFFI0161OWBW/), [IGVFFI2485QHCW](/sequence-files/IGVFFI2485QHCW/), [IGVFFI7660XDAA](/sequence-files/IGVFFI7660XDAA/), [IGVFFI3022SAZV](/sequence-files/IGVFFI3022SAZV/), [IGVFFI6127EKXN](/sequence-files/IGVFFI6127EKXN/), [IGVFFI4723JMWA](/sequence-files/IGVFFI4723JMWA/), [IGVFFI7162NMEV](/sequence-files/IGVFFI7162NMEV/), [IGVFFI6297TFMW](/sequence-files/IGVFFI6297TFMW/), [IGVFFI1019IHWR](/sequence-files/IGVFFI1019IHWR/), [IGVFFI6805RFPJ](/sequence-files/IGVFFI6805RFPJ/), [IGVFFI8388ENWV](/sequence-files/IGVFFI8388ENWV/), [IGVFFI7126BEZG](/sequence-files/IGVFFI7126BEZG/), [IGVFFI0088UADS](/sequence-files/IGVFFI0088UADS/), [IGVFFI3273CLCU](/sequence-files/IGVFFI3273CLCU/), [IGVFFI4532XBOH](/sequence-files/IGVFFI4532XBOH/), [IGVFFI2621TQRQ](/sequence-files/IGVFFI2621TQRQ/), [IGVFFI0937JKTX](/sequence-files/IGVFFI0937JKTX/), [IGVFFI4233IDKO](/sequence-files/IGVFFI4233IDKO/), [IGVFFI7807UKYJ](/sequence-files/IGVFFI7807UKYJ/), [IGVFFI4009KRZP](/sequence-files/IGVFFI4009KRZP/), [IGVFFI9325LKZS](/sequence-files/IGVFFI9325LKZS/), [IGVFFI2530EQUG](/sequence-files/IGVFFI2530EQUG/), [IGVFFI4326RSEE](/sequence-files/IGVFFI4326RSEE/), [IGVFFI6132IGDK](/sequence-files/IGVFFI6132IGDK/), [IGVFFI4219BQNZ](/sequence-files/IGVFFI4219BQNZ/), [IGVFFI6452YQQQ](/sequence-files/IGVFFI6452YQQQ/), [IGVFFI0680QOKE](/sequence-files/IGVFFI0680QOKE/), [IGVFFI5369CUSP](/sequence-files/IGVFFI5369CUSP/), [IGVFFI4238ROJZ](/sequence-files/IGVFFI4238ROJZ/), [IGVFFI1671NGBR](/sequence-files/IGVFFI1671NGBR/), [IGVFFI4206IKEE](/sequence-files/IGVFFI4206IKEE/), [IGVFFI3395SYDN](/sequence-files/IGVFFI3395SYDN/), [IGVFFI6643RXYS](/sequence-files/IGVFFI6643RXYS/), [IGVFFI5129FTIF](/sequence-files/IGVFFI5129FTIF/), [IGVFFI8695EBLD](/sequence-files/IGVFFI8695EBLD/), [IGVFFI3854ANZB](/sequence-files/IGVFFI3854ANZB/), [IGVFFI7844RDQK](/sequence-files/IGVFFI7844RDQK/), [IGVFFI9885WAYR](/sequence-files/IGVFFI9885WAYR/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS8629CPYB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8629CPYB](/measurement-sets/IGVFDS8629CPYB/) has sequence file(s): [IGVFFI8994EWVT](/sequence-files/IGVFFI8994EWVT/), [IGVFFI2651MBBL](/sequence-files/IGVFFI2651MBBL/), [IGVFFI7102LRYO](/sequence-files/IGVFFI7102LRYO/), [IGVFFI7634THJL](/sequence-files/IGVFFI7634THJL/), [IGVFFI8835LGFN](/sequence-files/IGVFFI8835LGFN/), [IGVFFI0604FIKB](/sequence-files/IGVFFI0604FIKB/), [IGVFFI1286NYQN](/sequence-files/IGVFFI1286NYQN/), [IGVFFI9104WBGE](/sequence-files/IGVFFI9104WBGE/), [IGVFFI6520TEPW](/sequence-files/IGVFFI6520TEPW/), [IGVFFI9851JPHD](/sequence-files/IGVFFI9851JPHD/), [IGVFFI0161OWBW](/sequence-files/IGVFFI0161OWBW/), [IGVFFI2485QHCW](/sequence-files/IGVFFI2485QHCW/), [IGVFFI7660XDAA](/sequence-files/IGVFFI7660XDAA/), [IGVFFI3022SAZV](/sequence-files/IGVFFI3022SAZV/), [IGVFFI6127EKXN](/sequence-files/IGVFFI6127EKXN/), [IGVFFI4723JMWA](/sequence-files/IGVFFI4723JMWA/), [IGVFFI7162NMEV](/sequence-files/IGVFFI7162NMEV/), [IGVFFI6297TFMW](/sequence-files/IGVFFI6297TFMW/), [IGVFFI1019IHWR](/sequence-files/IGVFFI1019IHWR/), [IGVFFI6805RFPJ](/sequence-files/IGVFFI6805RFPJ/), [IGVFFI8388ENWV](/sequence-files/IGVFFI8388ENWV/), [IGVFFI7126BEZG](/sequence-files/IGVFFI7126BEZG/), [IGVFFI0088UADS](/sequence-files/IGVFFI0088UADS/), [IGVFFI3273CLCU](/sequence-files/IGVFFI3273CLCU/), [IGVFFI4532XBOH](/sequence-files/IGVFFI4532XBOH/), [IGVFFI2621TQRQ](/sequence-files/IGVFFI2621TQRQ/), [IGVFFI0937JKTX](/sequence-files/IGVFFI0937JKTX/), [IGVFFI4233IDKO](/sequence-files/IGVFFI4233IDKO/), [IGVFFI7807UKYJ](/sequence-files/IGVFFI7807UKYJ/), [IGVFFI4009KRZP](/sequence-files/IGVFFI4009KRZP/), [IGVFFI9325LKZS](/sequence-files/IGVFFI9325LKZS/), [IGVFFI2530EQUG](/sequence-files/IGVFFI2530EQUG/), [IGVFFI4326RSEE](/sequence-files/IGVFFI4326RSEE/), [IGVFFI6132IGDK](/sequence-files/IGVFFI6132IGDK/), [IGVFFI4219BQNZ](/sequence-files/IGVFFI4219BQNZ/), [IGVFFI6452YQQQ](/sequence-files/IGVFFI6452YQQQ/), [IGVFFI0680QOKE](/sequence-files/IGVFFI0680QOKE/), [IGVFFI5369CUSP](/sequence-files/IGVFFI5369CUSP/), [IGVFFI4238ROJZ](/sequence-files/IGVFFI4238ROJZ/), [IGVFFI1671NGBR](/sequence-files/IGVFFI1671NGBR/), [IGVFFI4206IKEE](/sequence-files/IGVFFI4206IKEE/), [IGVFFI3395SYDN](/sequence-files/IGVFFI3395SYDN/), [IGVFFI6643RXYS](/sequence-files/IGVFFI6643RXYS/), [IGVFFI5129FTIF](/sequence-files/IGVFFI5129FTIF/), [IGVFFI8695EBLD](/sequence-files/IGVFFI8695EBLD/), [IGVFFI3854ANZB](/sequence-files/IGVFFI3854ANZB/), [IGVFFI7844RDQK](/sequence-files/IGVFFI7844RDQK/), [IGVFFI9885WAYR](/sequence-files/IGVFFI9885WAYR/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS8629CPYB/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0450DIVA](/in-vitro-systems/IGVFSM0450DIVA/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM0450DIVA/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0450DIVA](/in-vitro-systems/IGVFSM0450DIVA/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM0450DIVA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8629CPYB](/measurement-sets/IGVFDS8629CPYB/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS8629CPYB/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"file_set_type": "guide library",
"status": "in progress",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:11.677675+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI8994EWVT/",
"accession": "IGVFFI8994EWVT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep12_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:08:00.656032+00:00",
"file_format": "fastq",
"file_size": 799338,
"href": "/sequence-files/IGVFFI8994EWVT/@@download/IGVFFI8994EWVT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b2893568-33c2-46d0-9105-5e973f052da4/IGVFFI8994EWVT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep12_S318_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2651MBBL/",
"accession": "IGVFFI2651MBBL",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep11_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:07:20.132826+00:00",
"file_format": "fastq",
"file_size": 756613,
"href": "/sequence-files/IGVFFI2651MBBL/@@download/IGVFFI2651MBBL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c58821a5-11f8-4da2-8b37-70d1409e4c4c/IGVFFI2651MBBL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep11_S317_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7102LRYO/",
"accession": "IGVFFI7102LRYO",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep10_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:06:33.264148+00:00",
"file_format": "fastq",
"file_size": 892136,
"href": "/sequence-files/IGVFFI7102LRYO/@@download/IGVFFI7102LRYO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/10e0bb83-86a1-4ac1-9871-a0412536224f/IGVFFI7102LRYO.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep10_S316_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7634THJL/",
"accession": "IGVFFI7634THJL",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep12_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:08:19.118453+00:00",
"file_format": "fastq",
"file_size": 3588782,
"href": "/sequence-files/IGVFFI7634THJL/@@download/IGVFFI7634THJL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bacf9663-3205-4fa8-9633-0954078a112e/IGVFFI7634THJL.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep12_S318_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8835LGFN/",
"accession": "IGVFFI8835LGFN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:10:46.618132+00:00",
"file_format": "fastq",
"file_size": 3554132,
"href": "/sequence-files/IGVFFI8835LGFN/@@download/IGVFFI8835LGFN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/93dd4ac9-e0ce-47cb-8b22-dadf3fb36ecf/IGVFFI8835LGFN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep5_S221_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0604FIKB/",
"accession": "IGVFFI0604FIKB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep5_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:10:27.900765+00:00",
"file_format": "fastq",
"file_size": 800278,
"href": "/sequence-files/IGVFFI0604FIKB/@@download/IGVFFI0604FIKB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2d9066e4-3126-472a-9f3c-4afda4ab3a86/IGVFFI0604FIKB.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep5_S221_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1286NYQN/",
"accession": "IGVFFI1286NYQN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:09:41.440890+00:00",
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"file_size": 931898,
"href": "/sequence-files/IGVFFI1286NYQN/@@download/IGVFFI1286NYQN.fastq.gz",
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},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep4_S220_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9104WBGE/",
"accession": "IGVFFI9104WBGE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:12:00.428694+00:00",
"file_format": "fastq",
"file_size": 3632067,
"href": "/sequence-files/IGVFFI9104WBGE/@@download/IGVFFI9104WBGE.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6520TEPW/",
"accession": "IGVFFI6520TEPW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:09:14.210356+00:00",
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"file_size": 833481,
"href": "/sequence-files/IGVFFI6520TEPW/@@download/IGVFFI6520TEPW.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep3_S219_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9851JPHD/",
"accession": "IGVFFI9851JPHD",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep11_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:07:38.538953+00:00",
"file_format": "fastq",
"file_size": 3373715,
"href": "/sequence-files/IGVFFI9851JPHD/@@download/IGVFFI9851JPHD.fastq.gz",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep1-BinC-PCRrep11_S317_R2_001.fastq.gz",
"upload_status": "validated"
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"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T22:05:55.704308+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"symbol": "PPIF",
"synonyms": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "041a55b3-5702-4de8-b888-c3f66535ee9f"
}